2iqa

PFA2 FAB fragment, monoclinic apo form

Method: X-RAY DIFFRACTION Dmax: 129.2 Å Quality: REASONABLE

1. Protein Identity and Related Structures Protein Identity & Related Structures

IgG2a Fab fragment PFA2 Kappa light chain

OrganismNot specified

UniProt A2NHM3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain L; UniProt 1–219 Not recorded IgG2a Fab fragment PFA2 heavy chain × 1 (Q811U5) ACM ACETAMIDE × 1 GOL GLYCEROL × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;0.1 M Bis-Tris, 28% PEG-MME 2000, pH 6.5, VAPOR DIFFUSION Resolution 2.00 Å R-free 0.279
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–219 Not recorded IgG2a Fab fragment PFA2 heavy chain × 1 (Q811U5) ACM ACETAMIDE × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;0.1 M Bis-Tris, 28% PEG-MME 2000, pH 6.5, VAPOR DIFFUSION Resolution 2.00 Å R-free 0.279

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A2NHM3_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–219; UniProt 1–219 Author chain L; PDBConstruct 1–219; UniProt 1–219

IgG2a Fab fragment PFA2 heavy chain

OrganismNot specified

UniProt Q811U5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain H; UniProt 1–118 Not recorded IgG2a Fab fragment PFA2 Kappa light chain × 1 (A2NHM3) ACM ACETAMIDE × 1 GOL GLYCEROL × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;0.1 M Bis-Tris, 28% PEG-MME 2000, pH 6.5, VAPOR DIFFUSION Resolution 2.00 Å R-free 0.279
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1–118 Not recorded IgG2a Fab fragment PFA2 Kappa light chain × 1 (A2NHM3) ACM ACETAMIDE × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;0.1 M Bis-Tris, 28% PEG-MME 2000, pH 6.5, VAPOR DIFFUSION Resolution 2.00 Å R-free 0.279

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q811U5_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–123; UniProt 1–118 Author chain H; PDBConstruct 1–123; UniProt 1–118

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2iqa

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2iqa
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2iqa
Deposition date deposition_date2006-10-13
Structure title titlePFA2 FAB fragment, monoclinic apo form
Keywords keywordspfa2, wwddd, cdr, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.04
Radius of gyration Rg (electron density) rg_electron40.96
Forward intensity I(0) i0142388000.00
Molecular weight molecular_weight95963.0 kDa
Excluded volume excluded_volume119740 ų
Envelope volume envelope_volume166190 ų
Hydration-shell volume shell_volume36606 ų
Envelope diameter envelope_diameter137.0
Shell Rg shell_rg41.77
Envelope Rg envelope_rg40.82
Shape Rg shape_rg40.92
Total Rg total_rg41.16
Total atoms total_atoms6753
Residues n_residues847
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax129.2
Rg (real space) rg_real41.44
Rg uncertainty (real space) rg_real_error1.44
I(0) (real space) i0_real1.4240e+08
I(0) uncertainty (real space) i0_real_error2.4840e+06
Rg (reciprocal space) rg_reciprocal41.05
I(0) (reciprocal space) i0_reciprocal142300000.0000
Solution quality estimate total_estimate0.5681
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.0
Skewness Skewness skewness0.492
Kurtosis Kurtosis kurtosis-0.617
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9573000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 0.046; Positv: 1.000; Valcen: 0.727; Smooth: 0.007

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd2iqaa1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd2iqaa2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd2iqab_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd2iqah_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd2iqal1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd2iqal2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (8 domains)

Domain ID domain_id2iqaA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2iqaA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2iqaB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2iqaB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2iqaH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2iqaH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2iqaL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2iqaL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)